NCBI C++ ToolKit
Classes | Functions
parse.cpp File Reference
#include <ncbi_pch.hpp>
#include <algo/gnomon/gnomon_model.hpp>
#include <algo/gnomon/gnomon_exception.hpp>
#include <objects/general/Object_id.hpp>
#include "hmm.hpp"
#include "parse.hpp"
#include "hmm_inlines.hpp"
+ Include dependency graph for parse.cpp:

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Classes

struct  SRState
 

Functions

 USING_SCOPE (objects)
 
template<class L , class R >
bool s_TooFar (const L &left, const R &right, double score)
 
template<class Left , class Right >
bool s_EvaluateNewScore (const Left &left, const Right &right, double &rscore, bool &openrgn, bool rightanchor=false)
 
template<class L , class R >
bool s_ForwardStep (const L &left, R &right, int leftprot, int rightprot)
 
template<class L >
bool s_ForwardStep (const L &left, CIntron &right)
 
template<class L >
bool s_ForwardStep (const L &left, CIntergenic &right, bool rightanchor)
 
template<class L , class R >
void s_MakeStep (vector< L > &lvec, vector< R > &rvec, int leftprot, int rightprot)
 
template<class L >
void s_MakeStep (vector< L > &lvec, vector< CIntron > &rvec)
 
template<class L >
void s_MakeStep (const CSeqScores &seqscr, vector< L > &lvec, vector< CIntergenic > &rvec, bool rightanchor=false)
 
void s_MakeStep (const CSeqScores &seqscr, const CExonParameters &exon_params, EStrand strand, int point, vector< CIntergenic > &lvec, vector< CSingleExon > &rvec)
 
template<class R >
void s_MakeStep (const CSeqScores &seqscr, const CExonParameters &exon_params, EStrand strand, int point, vector< CIntergenic > &lvec, vector< R > rvec[][3])
 
template<class R >
void s_MakeStep (const CSeqScores &seqscr, const CExonParameters &exon_params, EStrand strand, int point, vector< CIntron > lvec[][3], vector< R > &rvec)
 
void s_MakeStep (const CSeqScores &seqscr, const CExonParameters &exon_params, EStrand strand, int point, vector< CIntron > lvec[][3], vector< CInternalExon > rvec[][3])
 
template<class L1 , class L2 >
void s_MakeStep (const CSeqScores &seqscr, const CIntronParameters &intron_params, EStrand strand, int point, vector< L1 > lvec1[][3], vector< L2 > lvec2[][3], vector< CIntron > rvec[][3], int shift)
 
double AddProbabilities (double scr1, double scr2)
 
template<class T >
void Out (T t, int w, CNcbiOstream &to=cout)
 
void Out (double t, int w, CNcbiOstream &to=cout, int prec=1)
 
void AddSupport (const TGeneModelList &align_list, TSignedSeqRange inside_range, CGeneModel &gene, TSignedSeqRange reading_frame)
 

Function Documentation

double AddProbabilities ( double  scr1,
double  scr2 
)

Definition at line 325 of file parse.cpp.

References BadScore().

Referenced by CParse::CParse().

void AddSupport ( const TGeneModelList align_list,
TSignedSeqRange  inside_range,
CGeneModel gene,
TSignedSeqRange  reading_frame 
)
template<class T >
void Out ( T  t,
int  w,
CNcbiOstream to = cout 
)
void Out ( double  t,
int  w,
CNcbiOstream to = cout,
int  prec = 1 
)

Definition at line 474 of file parse.cpp.

template<class Left , class Right >
bool s_EvaluateNewScore ( const Left &  left,
const Right &  right,
double &  rscore,
bool openrgn,
bool  rightanchor = false 
)
inline

Definition at line 69 of file parse.cpp.

References BadScore(), and len.

Referenced by s_ForwardStep().

template<class L , class R >
bool s_ForwardStep ( const L &  left,
R right,
int  leftprot,
int  rightprot 
)
inline

Definition at line 121 of file parse.cpp.

References BadScore(), and s_EvaluateNewScore().

Referenced by s_MakeStep().

template<class L >
bool s_ForwardStep ( const L &  left,
CIntron right 
)
inline
template<class L >
bool s_ForwardStep ( const L &  left,
CIntergenic right,
bool  rightanchor 
)
inline
template<class L , class R >
void s_MakeStep ( vector< L > &  lvec,
vector< R > &  rvec,
int  leftprot,
int  rightprot 
)
inline

Definition at line 198 of file parse.cpp.

References i, and s_ForwardStep().

Referenced by CParse::CParse(), and s_MakeStep().

template<class L >
void s_MakeStep ( vector< L > &  lvec,
vector< CIntron > &  rvec 
)
inline

Definition at line 211 of file parse.cpp.

References i, kTooFarLen, max(), s_ForwardStep(), and CHMM_State::Stop().

template<class L >
void s_MakeStep ( const CSeqScores seqscr,
vector< L > &  lvec,
vector< CIntergenic > &  rvec,
bool  rightanchor = false 
)
inline
void s_MakeStep ( const CSeqScores seqscr,
const CExonParameters exon_params,
EStrand  strand,
int  point,
vector< CIntergenic > &  lvec,
vector< CSingleExon > &  rvec 
)
inline

Definition at line 254 of file parse.cpp.

References BadScore(), and s_MakeStep().

template<class R >
void s_MakeStep ( const CSeqScores seqscr,
const CExonParameters exon_params,
EStrand  strand,
int  point,
vector< CIntergenic > &  lvec,
vector< R rvec[][3] 
)
inline

Definition at line 262 of file parse.cpp.

References BadScore(), R, and s_MakeStep().

template<class R >
void s_MakeStep ( const CSeqScores seqscr,
const CExonParameters exon_params,
EStrand  strand,
int  point,
vector< CIntron lvec[][3],
vector< R > &  rvec 
)
inline

Definition at line 276 of file parse.cpp.

References BadScore(), R, and s_MakeStep().

void s_MakeStep ( const CSeqScores seqscr,
const CExonParameters exon_params,
EStrand  strand,
int  point,
vector< CIntron lvec[][3],
vector< CInternalExon rvec[][3] 
)
inline

Definition at line 289 of file parse.cpp.

References BadScore(), and s_MakeStep().

template<class L1 , class L2 >
void s_MakeStep ( const CSeqScores seqscr,
const CIntronParameters intron_params,
EStrand  strand,
int  point,
vector< L1 >  lvec1[][3],
vector< L2 >  lvec2[][3],
vector< CIntron rvec[][3],
int  shift 
)
inline

Definition at line 309 of file parse.cpp.

References BadScore(), and s_MakeStep().

template<class L , class R >
bool s_TooFar ( const L &  left,
const R right,
double  score 
)
inline

Definition at line 47 of file parse.cpp.

References BadScore(), kTooFarLen, and len.

Referenced by s_ForwardStep().

USING_SCOPE ( objects  )
Modified on Wed Nov 22 17:06:13 2017 by modify_doxy.py rev. 546573